6ND1: Sec Complex from yeast
CryoEM structure of the Sec Complex from yeast. Determined by electron microscopy at 4.1 Å resolution. Released 9 Jan 2019.
- Method
- Electron microscopy
- Resolution
- 4.1 Å
- Organism
- Saccharomyces cerevisiae
- Chains
- 6
- Atoms
- 9,186
- Mol. weight
- 193.39 kDa
- Released
- 9 Jan 2019
Explore 6ND1 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6ND1 contains 58 α-helices and 21 β-strands across 6 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
Chain A: 25 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 16-20 | 5 | |
| α-helix | 30-35 | 6 | |
| α-helix | 60-63 | 4 | |
| α-helix | 69-77 | 9 | |
| α-helix | 89-109 | 21 | |
| α-helix | 222-228 | 7 | |
| α-helix | 229-234 | 6 | |
| α-helix | 235-245 | 11 | |
| α-helix | 256-267 | 12 | |
| α-helix | 274-275 | 2 | |
| α-helix | 277-285 | 9 | |
| α-helix | 299-310 | 12 | |
| α-helix | 319-327 | 9 | |
| α-helix | 329-340 | 12 | |
| α-helix | 347-359 | 13 | |
| α-helix | 369-372 | 4 | |
| α-helix | 379-385 | 7 | |
| α-helix | 392-396 | 5 | |
| α-helix | 400-406 | 7 | |
| α-helix | 412-423 | 12 | |
| β-strand | 427 | 1 | 5 |
| β-strand | 430-436 | 7 | 6 |
| β-strand | 450-455 | 6 | 6 |
| β-strand | 458 | 1 | 5 |
| α-helix | 477-478 | 2 | |
| α-helix | 481-483 | 3 | |
| α-helix | 487-493 | 7 | |
| α-helix | 496-498 | 3 | |
| β-strand | 499 | 1 | 7 |
| β-strand | 510 | 1 | 7 |
| β-strand | 513-519 | 7 | 8 |
| β-strand | 524-525 | 2 | 8 |
| β-strand | 530-532 | 3 | 8 |
| α-helix | 538-540 | 3 | |
| β-strand | 569-574 | 6 | 6 |
| β-strand | 585-594 | 10 | 8 |
| β-strand | 602-609 | 8 | 8 |
Chain B: 19 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 20 | 1 | 1 |
| α-helix | 21-23 | 3 | |
| α-helix | 26-28 | 3 | |
| α-helix | 29-47 | 19 | |
| β-strand | 50 | 1 | 2 |
| α-helix | 51 | 1 | |
| α-helix | 66-70 | 5 | |
| β-strand | 76 | 1 | 2 |
| α-helix | 83-92 | 10 | |
| α-helix | 116-136 | 21 | |
| α-helix | 147-173 | 27 | |
| α-helix | 180-197 | 18 | |
| β-strand | 198-203 | 6 | 3 |
| β-strand | 210-213 | 4 | 3 |
| α-helix | 216-222 | 7 | |
| α-helix | 230-237 | 8 | |
| α-helix | 244-261 | 18 | |
| β-strand | 264-269 | 6 | 4 |
| β-strand | 279-284 | 6 | 4 |
| α-helix | 287-290 | 4 | |
| α-helix | 291-313 | 23 | |
| α-helix | 348-349 | 2 | |
| α-helix | 359-383 | 25 | |
| α-helix | 388-398 | 11 | |
| β-strand | 402 | 1 | 4 |
| α-helix | 410-439 | 30 | |
| α-helix | 445-463 | 19 | |
Chain C: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 27-35 | 9 | |
| α-helix | 44-79 | 36 | |
Chain D: 2 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 38-46 | 9 | |
| β-strand | 52 | 1 | 1 |
| α-helix | 56-74 | 19 | |
Chain E: 5 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 31-59 | 29 | |
| α-helix | 71-80 | 10 | |
| α-helix | 93-123 | 31 | |
| α-helix | 128-152 | 25 | |
| α-helix | 160-175 | 16 | |
Chain F: 5 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 102-119 | 18 | |
| α-helix | 123-135 | 13 | |
| α-helix | 140-151 | 12 | |
| α-helix | 157-169 | 13 | |
| α-helix | 176-191 | 16 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Protein transport protein SEC61 | B | protein | 480 | Saccharomyces cerevisiae | P32915 (AlphaFold model) |
| Protein translocation protein SEC63 | A | protein | 677 | Saccharomyces cerevisiae | P14906 (AlphaFold model) |
| Protein transport protein SSS1 | C | protein | 80 | Saccharomyces cerevisiae | P35179 (AlphaFold model) |
| Protein transport protein SBH1 | D | protein | 82 | Saccharomyces cerevisiae | P52870 (AlphaFold model) |
| Translocation protein SEC66 | E | protein | 206 | Saccharomyces cerevisiae | P33754 |
| Translocation protein SEC72 | F | protein | 193 | Saccharomyces cerevisiae | P39742 |
Sequence of entity 1 (B), FASTA
>6ND1_1 Protein transport protein SEC61 (chains B)
MSSNRVLDLFKPFESFLPEVIAPERKVPYNQKLIWTGVSLLIFLILGQIPLYGIVSSETS
DPLYWLRAMLASNRGTLLELGVSPIITSSMIFQFLQGTQLLQIRPESKQDRELFQIAQKV
CAIILILGQALVVVMTGNYGAPSDLGLPICLLLIFQLMFASLIVMLLDELLSKGYGLGSG
ISLFTATNIAEQIFWRAFAPTTVNSGRGKEFEGAVIAFFHLLAVRKDKKRALVEAFYRTN
LPNMFQVLMTVAIFLFVLYLQGFRYELPIRSTKVRGQIGIYPIKLFYTSNTPIMLQSALT
SNIFLISQILFQKYPTNPLIRLIGVWGIRPGTQGPQMALSGLAYYIQPLMSLSEALLDPI
KTIVYITFVLGSCAVFSKTWIEISGTSPRDIAKQFKDQGMVINGKRETSIYRELKKIIPT
AAAFGGATIGALSVGSDLLGTLGSGASILMATTTIYGYYEAAAKEGGFTKNLVPGFSDLM
Sequence of entity 2 (A), FASTA
>6ND1_2 Protein translocation protein SEC63 (chains A)
MPTNYEYDEASETWPSFILTGLLMVVGPMTLLQIYQIFFGANAEDGNSGKSKEFNEEVFK
NLNEEYTSDEIKQFRRKFDKNSNKKSKIWSRRNIIIIVGWILVAILLQRINSNDAIKDAA
TKLFDPYEILGISTSASDRDIKSAYRKLSVKFHPDKLAKGLTPDEKSVMEETYVQITKAY
ESLTDELVRQNYLKYGHPDGPQSTSHGIALPRFLVDGSASPLLVVCYVALLGLILPYFVS
RWWARTQSYTKKGIHNVTASNFVSNLVNYKPSEIVTTDLILHWLSFAHEFKQFFPDLQPT
DFEKLLQDHINRRDSGKLNNAKFRIVAKCHSLLHGLLDIACGFRNLDIALGAINTFKCIV
QAVPLTPNCQILQLPNVDKEHFITKTGDIHTLGKLFTLEDAKIGEVLGIKDQAKLNETLR
VASHIPNLKIIKADFLVPGENQVTPSSTPYISLKVLVRSAKQPLIPTSLIPEENLTEPQD
FESQRDPFAMMSKQPLVPYSFAPFFPTKRRGSWCCLVSSQKDGKILQTPIIIEKLSYKNL
NDDKDFFDKRIKMDLTKHEKFDINDWEIGTIKIPLGQPAPETVGDFFFRVIVKSTDYFTT
DLDITMNMKVRDSPAVEQVEVYSEEDDEYSTDDDETESDDESDASDYTDIDTDTEAEDDE
SPEGSGGSGDYKDDDDK
Sequence of entity 3 (C), FASTA
>6ND1_3 Protein transport protein SSS1 (chains C)
MARASEKGEEKKQSNNQVEKLVEAPVEFVREGTQFLAKCKKPDLKEYTKIVKAVGIGFIA
VGIIGYAIKLIHIPIRYVIV
Sequence of entity 4 (D), FASTA
>6ND1_4 Protein transport protein SBH1 (chains D)
MSSPTPPGGQRTLQKRKQGSSQKVAASAPKKNTNSNNSILKIYSDEATGLRVDPLVVLFL
AVGFIFSVVALHVISKVAGKLF
Sequence of entity 5 (E), FASTA
>6ND1_5 Translocation protein SEC66 (chains E)
MSEFNETKFSNNGTFFETEEPIVETKSISVYTPLIYVFILVVSLVMFASSYRKKQAKKIS
EQPSIFDENDAHDLYFQIKEMSENEKIHEKVLKAALLNRGAESVRRSLKLKELAPQINLL
YKNGSIGEDYWKRFETEVKLIELEFKDTLQEAERLQPGWVQLFVMVCKEICFNQALSRRY
QSILKRKEVCIKEWELKINNDGRLVN
Sequence of entity 6 (F), FASTA
>6ND1_6 Translocation protein SEC72 (chains F)
MVTLEYNANSKLITASDAVVALSTETNIDQINVLTTSLIGETNPNFTPQPNEALSKMIKG
LFESGMKNLQQKKLNEALKNVSLAIEMAQRKRAPWEAFAIQLPELHFMLRSKIDLCLILG
KHLEALQDLDFLLGTGLIQPDVFVRKADCLLKLRQWEEARATCERGLALAPEDMKLRALL
IETARNLAEYNGE
Primary citation
Structure of the post-translational protein translocation machinery of the ER membrane. Wu, X., Cabanos, C., Rapoport, T.A. Nature (2019) 566:136-139. DOI 10.1038/s41586-018-0856-x · PubMed
Other PDB entries of the same protein (UniProt P32915 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 7KAH 3.1 Å, Cryo-EM structure of the Sec complex from S. cerevisiae, wild-type, class without Sec62
- 7KAJ 3.1 Å, Cryo-EM structure of the Sec complex from S. cerevisiae, wild-type, class with Sec62,…
- 7KAI 3.2 Å, Cryo-EM structure of the Sec complex from S. cerevisiae, wild-type, class with Sec62,…
- 6N3Q 3.68 Å, Cryo-EM structure of the yeast Sec complex
- 7KB5 3.8 Å, Cryo-EM structure of the Sec complex from yeast, Sec63 FN3 and residues 210-216 mutated
- 7KAS 3.9 Å, Cryo-EM structure of the Sec complex from S. cerevisiae, Sec63 FN3 mutant, class with…
- 7KAO 4.0 Å, Cryo-EM structure of the Sec complex from S. cerevisiae, Sec61 pore mutant, class…
- 7KAQ 4.0 Å, Cryo-EM structure of the Sec complex from S. cerevisiae, Sec61 pore mutant, class with…
- 7KAR 4.0 Å, Cryo-EM structure of the Sec complex from S. cerevisiae, Sec63 FN3 mutant, class without…
- 7KAU 4.0 Å, Cryo-EM structure of the Sec complex from S. cerevisiae, Sec61 pore ring and Sec63 FN3…
- 7KAP 4.1 Å, Cryo-EM structure of the Sec complex from S. cerevisiae, Sec61 pore mutant, class with…
- 7AFT 4.4 Å, Cryo-EM structure of the signal sequence-engaged post-translational Sec translocon
Browse structure collections
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